Genes Involved in Differentiation, Stem Cell Renewal, and Tumorigenesis Are Modulated in Telomerase- Immortalized Human Urothelial Cells

Total Page:16

File Type:pdf, Size:1020Kb

Genes Involved in Differentiation, Stem Cell Renewal, and Tumorigenesis Are Modulated in Telomerase- Immortalized Human Urothelial Cells Genes Involved in Differentiation, Stem Cell Renewal, and Tumorigenesis Are Modulated in Telomerase- Immortalized Human Urothelial Cells Emma J. Chapman,1 Gavin Kelly,2 and Margaret A. Knowles1 1Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds, United Kingdom and 2Bioinformatics and Biostatistics Service, Cancer Research UK, London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom Abstract non–telomere effects of telomerase and provides further The expression of hTERT, the catalytic subunit of rationale for the use of telomerase inhibitors in UC. telomerase, immortalizes normal human urothelial cells (Mol Cancer Res 2008;6(7):1154–68) (NHUC). Expression of a modified hTERT, without the ability to act in telomere maintenance, did not Introduction immortalize NHUC, confirming that effects at telomeres The primary and well-documented role of telomerase is as are required for urothelial immortalization. Previous a reverse transcriptase that acts in the maintenance of studies indicate that inhibition of telomerase has an telomere length and structure. Up-regulation of telomerase immediate effect on urothelial carcinoma (UC) cell line expression occurs in the majority of urothelial carcinoma viability, before sufficient divisions to account for (UC) irrespective or stage or grade (1), suggesting that this telomere attrition, implicating non–telomere effects may be an early event in tumorigenesis. Normal human of telomerase in UC. We analyzed the effects of urothelial cells (NHUC) are immortalized by expression of telomerase on gene expression in isogenic mortal and hTERT, the catalytic subunit of telomerase. In contrast to hTERT-transduced NHUC. hTERT expression led to requirements for immortalization in other epithelial cell types consistent alterations in the expression of genes and despite the common loss of expression of p16 in UC, predicted to be of phenotypic significance in inactivation of the CDKN2A locus (encoding p16 and tumorigenesis. A subset of expression changes were p14ARF) was not observed (2). detected soon after transduction with hTERT and Non–telomere effects of hTERT expression have been persisted with continued culture. These genes (NME5, described in other cell types, some of which may be relevant to PSCA, TSPYL5, LY75, IGFBP2, IGF2, CEACAM6, XG, tumorigenesis in vivo (3, 4). Inhibition of telomerase as a NOX5, KAL1 HPGD , and ) include eight previously therapeutic strategy is generally based on the assumption that identified as polycomb group targets. TERT-NHUC lack of telomerase activity will result in continued cell division showed overexpression of the polycomb repressor and telomere attrition, which will eventually lead to replicative complex (PRC1 and PRC4) components, BMI1 and senescence or apoptosis (5). However, inhibition of telomerase SIRT1, and down-regulation of multiple PRC targets and has an immediate effect on UC cell line viability, before genes associated with differentiation. TERT-NHUC at 100 sufficient divisions to account for telomere attrition (6). This population doublings, but not soon after transduction, strongly implicates non–telomere effects of hTERT in bladder showed increased saturation density and an attenuated tumorigenesis and suggests that telomerase inhibition may be of differentiation response, indicating that these are not rapid therapeutic benefit. Thus, identification of the genes and acute effects of telomerase expression. Some of the pathways involved in the non–telomere effects of telomerase in changes in gene expression identified may contribute bladder and other cancers may highlight novel therapeutic or to tumorigenesis. Expression of NME5 and NDN was diagnostic targets. There is also data that links the expression of down-regulated in UC cell lines and tumors. Our data telomerase with the inhibition of cellular differentiation (7, 8). supports the concept of both telomere-based and This may be a non–telomere event and is an example of how telomerase expression could contribute to tumorigenesis by mechanisms discrete from its classic actions in telomere Received 11/19/07; revised 4/18/08; accepted 4/21/08. maintenance. Grant support: In part by Cancer Research UK (C6228/A5433). hTERT-immortalized NHUC (TERT-NHUC) are generally The costs of publication of this article were defrayed in part by the payment of diploid and have no chromosomal alterations (detectable by page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. array CGH or karyotyping; ref. 2). However, changes in gene Note: Supplementary data for this article are available at Molecular Cancer expression after telomerase expression have not been Research Online (http://mcr.aacrjournals.org/). investigated. Microarray analysis of gene expression in Requests for reprints: Margaret A. Knowles, Cancer Research UK Clinical Centre, St. James’s University Hospital, Beckett Street, Leeds LS97TF, United isogenic mortal NHUC and their hTERT-immortalized coun- Kingdom. Phone: 44-11320-64913; Fax: 44-11324-29886. E-mail: m.a.knowles@ terparts was done to examine the hypothesis that expression of leeds.ac.uk Copyright D 2008 American Association for Cancer Research. telomerase contributes to tumorigenesis in ways that are doi:10.1158/1541-7786.MCR-07-2168 additional to its effect on telomere length and structure. As 1154 Mol Cancer Res 2008;6(7). July 2008 Downloaded from mcr.aacrjournals.org on October 1, 2021. © 2008 American Association for Cancer Research. Gene Expression Analysis of TERT-NHUC 1155 TERT-NHUC had no detectable genetic alterations, we aimed it is possible that more subtle effects on telomere structure such to identify changes in gene expression that may have occurred as at the 3¶ overhang are required for immortalization (14). To via transcriptional mechanisms. Additionally, as TERT-NHUC determine whether immortalization of NHUC was due to effects provide the basis for an in vitro model of urothelial on telomere maintenance, cells were transduced to express transformation, it is important to determine whether alterations hTERT-HA. hTERT-HA has a carboxyl-terminal hemagglutinin in gene expression are present before other genes are (HA) tag and induces soluble telomerase activity but cannot act experimentally manipulated. in telomere maintenance, probably due to an inability to interact Several previous experiments have examined the effect of with the additional proteins required (15). Despite the induction hTERT on gene expression (9-12). There is little concordance of telomerase activity (7.2-fold compared with empty vector– between genes identified in these studies, which perhaps transduced cells), the expression of hTERT-HA did not lead to a reflects the cell type–specific pathways involved in immor- significant extension in the replicative life span of NHUC, talization. This is mirrored by the different combinations of confirming that telomere-dependent effects are required for the alterations seen in tumors arising within a particular tissue. immortalization of NHUC (Fig. 1). No previous study has examined changes in gene expression after telomerase expression in matched pairs of mortal and Telomerase Activity immortal epithelial cells from multiple donors. By repeating A low level of telomerase activity was detected in mortal the experiment in three biological replicates (derived from NHUC strains. Telomerase activity in each TERT-NHUC line three cell donors) and looking for changes in expression was quantified relative to that in the isogenic NHUC cell strain. consistent to multiple donors relative to their isogenic The ratios were 17, 9, and 6 for TERT-NHUC N, TERT-NHUC controls, inter-cell line differences should be minimal. This B, and TERT-NHUC A, respectively (Fig. 2A). experimental design should increase the power to detect genes whose expression is consistently altered after expres- Expression of hTERT Leads to Consistent and Stable sion of telomerase. We propose that the effects of telomerase Changes in Gene Expression in vivo are likely to be a combination and potentially Changes in gene expression of 2.0-fold or greater were synergistic effect of the classic actions in maintenance of identified following the comparison of hTERT-transduced and telomere length and structure coupled to its currently isogenic mortal strains of NHUC from three donors. This uncharacterized non–telomere effects. For this reason, we analysis was done soon after transduction with hTERT when chose to investigate the putative non–telomere effects of cells were still within their normal mortal life span [<18 telomerase in the biologically relevant context of fully population doublings (PD)] and also when cells were deemed functional telomerase. immortal and had undergone f100 and 250 PDs. The expression of hTERT led to a statistically significant down- Results regulation of 104 probe sets, early after transduction, in at Expression of a Modified hTERT without the Ability to least two of the three donors (Table 1). These comprised 87 Elongate Telomeres Does Not Immortalize NHUC genes and 17 unknown transcripts or open reading frames It has been unclear how expression of hTERT immortalizes (orf) or hypothetical genes. In cases in which a change in NHUC, as profound shortening of telomere length is not expression in cells from one of the three donors was not observed in NHUC at replicative senescence (2, 13). However, statistically
Recommended publications
  • Repeated BCG Treatment of Mouse Bladder Selectively Stimulates Small
    BMC Cancer BioMed Central Research article Open Access Repeated BCG treatment of mouse bladder selectively stimulates small GTPases and HLA antigens and inhibits single-spanning uroplakins Marcia R Saban1, Helen L Hellmich2, Cindy Simpson1, Carole A Davis1, Mark L Lang3, Michael A Ihnat4, Michael A O'Donnell5, Xue-Ru Wu6 and Ricardo Saban*1 Address: 1Department of Physiology, The University Oklahoma Health Sciences Center, Oklahoma City, USA, 2Department of Anesthesiology, University of Texas Medical Branch, Galveston, USA, 3Department of Microbiology and Immunology The University Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA, 4Department of Cell Biology, The University Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA, 5Department of Urology, University of Iowa, UI Hospitals and Clinics, Iowa City, Iowa 52242-1089, USA and 6Department of Urology, New York University, School of Medicine, New York, NY 10016, USA Email: Marcia R Saban - [email protected]; Helen L Hellmich - [email protected]; Cindy Simpson - [email protected]; Carole A Davis - [email protected]; Mark L Lang - [email protected]; Michael A Ihnat - [email protected]; Michael A O'Donnell - [email protected]; Xue-Ru Wu - [email protected]; Ricardo Saban* - [email protected] * Corresponding author Published: 2 November 2007 Received: 29 August 2007 Accepted: 2 November 2007 BMC Cancer 2007, 7:204 doi:10.1186/1471-2407-7-204 This article is available from: http://www.biomedcentral.com/1471-2407/7/204 © 2007 Saban et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • Hippo and Sonic Hedgehog Signalling Pathway Modulation of Human Urothelial Tissue Homeostasis
    Hippo and Sonic Hedgehog signalling pathway modulation of human urothelial tissue homeostasis Thomas Crighton PhD University of York Department of Biology November 2020 Abstract The urinary tract is lined by a barrier-forming, mitotically-quiescent urothelium, which retains the ability to regenerate following injury. Regulation of tissue homeostasis by Hippo and Sonic Hedgehog signalling has previously been implicated in various mammalian epithelia, but limited evidence exists as to their role in adult human urothelial physiology. Focussing on the Hippo pathway, the aims of this thesis were to characterise expression of said pathways in urothelium, determine what role the pathways have in regulating urothelial phenotype, and investigate whether the pathways are implicated in muscle-invasive bladder cancer (MIBC). These aims were assessed using a cell culture paradigm of Normal Human Urothelial (NHU) cells that can be manipulated in vitro to represent different differentiated phenotypes, alongside MIBC cell lines and The Cancer Genome Atlas resource. Transcriptomic analysis of NHU cells identified a significant induction of VGLL1, a poorly understood regulator of Hippo signalling, in differentiated cells. Activation of upstream transcription factors PPARγ and GATA3 and/or blockade of active EGFR/RAS/RAF/MEK/ERK signalling were identified as mechanisms which induce VGLL1 expression in NHU cells. Ectopic overexpression of VGLL1 in undifferentiated NHU cells and MIBC cell line T24 resulted in significantly reduced proliferation. Conversely, knockdown of VGLL1 in differentiated NHU cells significantly reduced barrier tightness in an unwounded state, while inhibiting regeneration and increasing cell cycle activation in scratch-wounded cultures. A signalling pathway previously observed to be inhibited by VGLL1 function, YAP/TAZ, was unaffected by VGLL1 manipulation.
    [Show full text]
  • Rare Copy Number Variants Disrupt Genes Regulating Vascular Smooth Muscle Cell Adhesion and Contractility in Sporadic Thoracic Aortic Aneurysms and Dissections
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector ARTICLE Rare Copy Number Variants Disrupt Genes Regulating Vascular Smooth Muscle Cell Adhesion and Contractility in Sporadic Thoracic Aortic Aneurysms and Dissections Siddharth K. Prakash,1 Scott A. LeMaire,2,3 Dong-Chuan Guo,4 Ludivine Russell,2 Ellen S. Regalado,4 Hossein Golabbakhsh,4 Ralph J. Johnson,4 Hazim J. Safi,5 Anthony L. Estrera,5 Joseph S. Coselli,2,3 Molly S. Bray,1 Suzanne M. Leal,1 Dianna M. Milewicz,4 and John W. Belmont1,* Thoracic aortic aneurysms and dissections (TAAD) cause significant morbidity and mortality, but the genetic origins of TAAD remain largely unknown. In a genome-wide analysis of 418 sporadic TAAD cases, we identified 47 copy number variant (CNV) regions that were enriched in or unique to TAAD patients compared to population controls. Gene ontology, expression profiling, and network anal- ysis showed that genes within TAAD CNVs regulate smooth muscle cell adhesion or contractility and interact with the smooth muscle- specific isoforms of a-actin and b-myosin, which are known to cause familial TAAD when altered. Enrichment of these gene functions in rare CNVs was replicated in independent cohorts with sporadic TAAD (STAAD, n ¼ 387) and inherited TAAD (FTAAD, n ¼ 88). The over- all prevalence of rare CNVs (23%) was significantly increased in FTAAD compared with STAAD patients (Fisher’s exact test, p ¼ 0.03). Our findings suggest that rare CNVs disrupting smooth muscle adhesion or contraction contribute to both sporadic and familial disease.
    [Show full text]
  • Human Urinary Exosomes As Innate Immune Effectors
    BASIC RESEARCH www.jasn.org Human Urinary Exosomes as Innate Immune Effectors † † ‡ Thomas F. Hiemstra,* Philip D. Charles, Tannia Gracia, Svenja S. Hester,§ † ‡ | Laurent Gatto, Rafia Al-Lamki,* R. Andres Floto,* Ya Su, Jeremy N. Skepper, † ‡ Kathryn S. Lilley, and Fiona E. Karet Frankl *Department of Medicine, †Cambridge Centre for Proteome Research and Cambridge Systems Biology Centre, Department of Biochemistry, ‡Department of Medical Genetics, and |Multi-Imaging Centre, Department of Anatomy, University of Cambridge, Cambridge, United Kingdom; and §Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom ABSTRACT Exosomes are small extracellular vesicles, approximately 50 nm in diameter, derived from the endocytic pathway and released by a variety of cell types. Recent data indicate a spectrum of exosomal functions, including RNA transfer, antigen presentation, modulation of apoptosis, and shedding of obsolete protein. Exosomes derived from all nephron segments are also present in human urine, where their function is unknown. Although one report suggested in vitro uptake of exosomes by renal cortical collecting duct cells, most studies of human urinary exosomes have focused on biomarker discovery rather than exosome function. Here, we report results from in-depth proteomic analyses and EM showing that normal human urinary exosomes are significantly enriched for innate immune proteins that include antimicrobial proteins and peptides and bacterial and viral receptors. Urinary exosomes, but not the prevalent soluble urinary protein uromodulin (Tamm–Horsfall protein), potently inhibited growth of pathogenic and commensal Escherichia coli and induced bacterial lysis. Bacterial killing depended on exosome structural integrity and occurred optimally at the acidic pH typical of urine from omnivorous humans.
    [Show full text]
  • The Regulation of Self-Renewal in Normal Human Urothelial Cells
    The Regulation of Self-Renewal in Normal Human Urothelial Cells Lisa A. Kirkwood PhD University of York Department of Biology April 2012 Abstract The urinary tract is lined by a mitotically-quiescent, but highly regenerative epithelium, the urothelium. The mechanisms regulating urothelial regeneration are incompletely understood although autocrine stimulation of the Epidermal Growth Factor Receptor (EGFR) signalling pathway has been implicated. The hypothesis developed in this thesis is that urothelial homeostasis is regulated through resolution of interactive signal transduction networks downstream of local environmental cues, such as cell:cell contact. Here, canonical Wnt signalling was examined as a candidate key pathway due to the pivotal role of β-catenin in both nuclear transcription and intercellular adherens junctions. Normal human urothelial (NHU) cells isolated from surgical biopsies were grown as finite cell lines in monolayer culture. mRNA analysis from proliferating cultures inferred all components for a functional autocrine-activated canonical Wnt cascade were present. In proliferating cells, β-catenin was nuclear and Axin2 expression provided an objective hallmark of β-catenin/TCF transcription factor activity. This endogenous activity was not mediated by Wnt receptor activation, as Wnt ligand was produced in inactive (non-palmitylated) form in serum-free culture, but instead -catenin activation was driven via EGFR- mediated phosphorylation of GSK3 and inhibition of the β-catenin destruction complex. In quiescent, contact–inhibited cultures, β-catenin was seen to re- localise to the adherens junctions and GSK3β activity was re-established. Knock-down of β-catenin using RNA interference led to significant changes in p-ERK and p-AKT activity as well as an increase in E-cadherin protein expression.
    [Show full text]
  • Identification of the Rac Gtpase Activating Protein Rho GAP 22 As a New Akt Substrate Defines a Novel Mechanism for Insulin Regulation of Cell Motility
    Identification of the Rac GTPase Activating Protein Rho GAP 22 as a New Akt Substrate Defines a Novel Mechanism for Insulin Regulation of Cell Motility Alexander Francis Rowland Submitted for the degree of Doctor of Philosophy Garvan Institute of Medical Research & Faculty of Medicine University of New South Wales ABSTRACT Insulin exerts many of its metabolic actions via the canonical PI3K/Akt pathway leading to phosphorylation and 14-3-3 binding of key metabolic targets. Recognising this, the goal of my thesis was to identify novel actions of insulin. To accomplish this I have conducted a screen to identify insulin-responsive 14-3-3 binding phosphoproteins and in so doing have identified a GTPase Activating Protein (GAP) for Rac1 called Rho GAP 22. Insulin increased 14-3-3 binding to Rho GAP 22 by 4 fold and this effect was PI3Kinase and Akt dependent. Using semi-quantitative mass spectrometry we identified two putative 14-3-3 binding sites (Ser16 and Ser397) within Rho GAP 22 and insulin increased phosphorylation at both of these sites. Mutagenesis studies revealed a complex interplay in phosphorylation at these two sites. Mutating Ser16 to Ala almost completely abolished 14-3-3 binding to Rho GAP 22 in vivo but not in vitro. Phosphorylation of Ser16 both in vitro and in vivo was Akt-dependent and inhibition of Akt prevented 14-3-3 binding to Ser16 in vitro. A truncated Rho GAP 22 protein lacking the N-terminal PH domain and Ser16 interacted with 14-3-3 in vivo and this interaction was Akt dependent. The Ser397 site in Rho GAP 22 is located close to the GAP domain and so it is likely that phosphorylation at this site regulates GAP activity.
    [Show full text]
  • The Consensus Coding Sequences of Human Breast and Colorectal Cancers Tobias Sjöblom,1* Siân Jones,1* Laura D
    The Consensus Coding Sequences of Human Breast and Colorectal Cancers Tobias Sjöblom,1* Siân Jones,1* Laura D. Wood,1* D. Williams Parsons,1* Jimmy Lin,1 Thomas Barber,1 Diana Mandelker,1 Rebecca J. Leary,1 Janine Ptak,1 Natalie Silliman,1 Steve Szabo,1 Phillip Buckhaults,2 Christopher Farrell,2 Paul Meeh,2 Sanford D. Markowitz,3 Joseph Willis,4 Dawn Dawson,4 James K. V. Willson,5 Adi F. Gazdar,6 James Hartigan,7 Leo Wu,8 Changsheng Liu,8 Giovanni Parmigiani,9 Ben Ho Park,10 Kurtis E. Bachman,11 Nickolas Papadopoulos,1 Bert Vogelstein,1† Kenneth W. Kinzler,1† Victor E. Velculescu1† 1Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA. 2Department of Pathology and Microbiology, Center for Colon Cancer Research, and South Carolina Cancer Center, Division of Basic Research, University of South Carolina School of Medicine, Columbia, SC 29229, USA. 3Department of Medicine, Ireland Cancer Center, and Howard Hughes Medical Institute, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA. 4Department of Pathology and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA. 5Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 6Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 7Agencourt Bioscience Corporation, Beverly, MA 01915, USA. 8SoftGenetics LLC, State College, PA 16803, USA. 9Departments of Oncology, Biostatistics, and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
    [Show full text]
  • Analysis of Differential Gene Expression in Colorectal Cancer and Stroma Using Fluorescence- Activated Cell Sorting Purification
    Analysis of differential gene expression in colorectal cancer and stroma using fluorescence- activated cell sorting purification The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Smith, M J, A C Culhane, M Donovan, J C Coffey, B D Barry, M A Kelly, D G Higgins, et al. 2009. “Analysis of Differential Gene Expression in Colorectal Cancer and Stroma Using Fluorescence- Activated Cell Sorting Purification.” British Journal of Cancer 100 (9) (May 5): 1452–1464. doi:10.1038/sj.bjc.6604931. Published Version doi:10.1038/sj.bjc.6604931 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:28724495 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Genomics. Author manuscript; available in PMC 2009 June 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Genomics. 2008 June ; 91(6): 508±511. doi:10.1016/j.ygeno.2008.03.002. Functional Classification Analysis of Somatically Mutated Genes in Human Breast and Colorectal Cancers Thomas W. Chittenden*,1,2,3, Eleanor A. Howe*,1, Aedin C. Culhane1,2, Razvan Sultana1, Jennifer M. Taylor4, Chris Holmes3,5, and John Quackenbush1,2 1Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA 2Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA 3Department of Statistics, University of Oxford, Oxford, UK 4Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK 5MRC Mammalian Genetics Unit, Harwell, UK.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • ( 12 ) United States Patent ( 10 ) Patent No .: US 10,787,712 B2 Sjoblom Et Al
    USO10787712B2 ( 12 ) United States Patent ( 10 ) Patent No .: US 10,787,712 B2 Sjoblom et al . ( 45 ) Date of Patent : * Sep . 29 , 2020 ( 54 ) CONSENSUS CODING SEQUENCES OF ( 56 ) References Cited HUMAN BREAST AND COLORECTAL CANCERS U.S. PATENT DOCUMENTS 5,605,799 A 2/1997 White et al . ( 71 ) Applicant: The Johns Hopkins University , 8,741,573 B2 * 6/2014 Sjoblom C12Q 1/6886 Baltimore , MD (US ) 435 / 6.14 2001/0021502 Al 9/2001 Swift et al . ( 72 ) Inventors: Tobias Sjoblom , Uppsala ( SE ) ; Sian 2007/0017666 Al 1/2007 Song Jones , Baltimore , MD (US ); D. 2010/0316995 Al 12/2010 Sjoblom et al . Williams Parsons , Bellaire, TX ( US ) ; FOREIGN PATENT DOCUMENTS Laura D. Wood , Baltimore, MD ( US ) ; Jimmy Cheng - Ho Lin , Baltimore , MD EP 785216 7/1997 EP 2543739 1/2013 ( US ) ; Thomas Barber , Nobelsville , TN WO WO 199213103 8/1992 ( US ) ; Diana Mandelker , Baltimore , WO WO 200042436 7/2000 MD ( US ) ; Bert Vogelstein , Baltimore , WO WO 2001042504 6/2001 MD ( US ) ; Kenneth W. Kinzler , WO WO 2004082458 9/2004 Baltimore , MD (US ); Victor E. WO WO 2005113824 12/2005 Velculescu, Dayton , MD ( US ) WO WO 2014110408 7/2014 ( 73 ) Assignee : The Johns Hopkins University , OTHER PUBLICATIONS Baltimore , MD (US ) Allen et al . , “ + A2 : D33The role of molecular markers in the adjuvant Subject to any disclaimer , the term of this treatment of colorectal cancer ,” European Journal of Cancer . Supple ( * ) Notice : ment, Pergamon , Oxfor, GB , vol . 3 , No. 3 , Oct. 1 , 2005 . patent is extended or adjusted under 35 Arai et al ., “ The inv ( 11 ) ( p15222) chromosome translocation of de U.S.C.
    [Show full text]
  • Open Mithun Shah.Pdf
    The Pennsylvania State University The Graduate School Department of Molecular Medicine ROLE OF SPHINGOLIPID SIGNALING IN PATHOGENESIS OF LARGE GRANULAR LYMPHOCYTE LEUKEMIA A Dissertation in Molecular Medicine by Mithun Vinod Shah © 2009 Mithun Vinod Shah Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 ii The dissertation of Mithun Vinod Shah was reviewed and approved* by the following: Thomas P. Loughran, Jr. Professor of Medicine Dissertation Advisor Co-Chair of Committee Rosalyn B. Irby Assistant Professor of Medicine Co-chair of Committee Gary Clawson Professor of Pathology, and Biochemistry and Molecular Biology Edward J. Gunther Assistant Professor of Medicine Charles H. Lang Director, Molecular Medicine Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Large granular lymphocyte (LGL) leukemia is a disorder of mature cytotoxic cells. LGL leukemia is characterized by accumulation of cytotoxic cells in blood and infiltration in bone marrow and other tissues. Leukemic LGL could arise from expansion of either CD3+ CD8+ T-cells (T-cell LGL leukemia or T-LGL leukemia) or those arising from CD3- natural killer (NK)-cells (NK-cell LGL leukemia or NK-LGL leukemia). LGL leukemia is a rare disorder consisting of less than 5% of non-B cell leukemia. Clinically, LGL leukemia can manifest along a spectrum of disorders ranging from slowly progressing indolent disorder to an aggressive leukemia that could be fatal within months. About fifty percent of LGL leukemia patients also present with variety of autoimmune conditions, rheumatoid arthritis being the most common one. Normally, following antigen clearance, cytotoxic T-lymphocytes (CTL) become sensitive to Fas-mediated apoptosis resulting in activation-induced cell death (AICD).
    [Show full text]
  • A Validation and Extended Description of the Lund Taxonomy for Urothelial
    www.nature.com/scientificreports OPEN A validation and extended description of the Lund taxonomy for urothelial carcinoma using the Received: 11 July 2017 Accepted: 19 February 2018 TCGA cohort Published: xx xx xxxx Nour-al-dain Marzouka1, Pontus Eriksson1, Carlos Rovira1, Fredrik Liedberg2, Gottfrid Sjödahl2 & Mattias Höglund1 Global gene expression analysis has been a major tool for urothelial carcinoma subtype discovery. This approach has revealed extensive complexity both in intrinsic features of the tumor cells and in the microenvironment. However, global gene expression cannot distinguish between gene expression signals originating from the tumor cells proper and from normal cells in the biopsy. Here, we use a large cohort of advanced urothelial carcinomas for which both gene expression data and extensive immunohistochemistry are available to create a supervised mRNA expression centroid classifer. This classifer identifes the major Lund taxonomy tumor cell phenotypes as defned by IHC. We apply this classifer to the independent TCGA dataset and show excellent associations between identifed subtypes and genomic features. We validate a progressed version of Urothelial-like A (UroA-Prog) that shows FGFR3 mutations and CDKN2A deletions, and we show that the variant Urothelial-like C is almost devoid of FGFR3 mutations. We show that Genomically Unstable tumors are very distinct from Urothelial-like tumors at the genomic level, and that tumors classifed as Basal/SCC-like all complied with the established defnition for Basal/SCC-like tumors. We identify the Mesenchymal-like and Small- cell/Neuroendocrine-like subtypes, and demonstrate that patients with UroB and Sc/NE-like tumors show the worst overall survival.
    [Show full text]